The home secretary, Theresa May, is expected to face questions in the Commons centred on the scale of reduced passport checks against the Home Office's "warning index" for potential terrorists and illegal migrants entering Britain.

Home Office sources confirmed on Friday that the warning index checks had been suspended at the port of Calais but there is growing speculation that these national security checks were also dropped at other ports and airports.

Downing Street said on Monday that David Cameron was "informed when it was apparent there was a problem" in the past few days and was not told of the original departmental decision in June to relax passport checks on UK and European biometric passport holders entering Britain.

The prime minister's spokesman stressed that Cameron continues to have "full confidence" in May and that she has not offered her resignation.

As the row continued to develop it emerged that the home secretary has also been forced to comply with a supreme court human rights ruling lifting a ban on British residents bringing spouses aged 18 to 21 to the UK to get married.

The ban, which is to be lifted from 28 November, is believed to affect 4,000 to 5,000 couples a year who apply for marriage visas.

The immigration minister, Damian Green, said they were "extremely disappointed that this change has been forced upon us" and claimed it would have an adverse impact on young victims of forced marriage.

Three UK Border Agency (UKBA) officials, including its head, Brodie Clark, were suspended last Thursday amid allegations that they went beyond ministerial authority and relaxed passport checks on travellers with non-European passports to cope with lengthening queues at Britain's ports and airports over the summer.

The four-month pilot scheme, which began in June and was only halted last week, also included the suspension of warning index checks at Calais. But evidence from whistleblowers inside UKBA suggests that the anti-terror checks may have also been suspended at other airports as well.

Number 10 said on Monday it regarded the relaxation of border controls for the UK and EU passport holders as a departmental decision that did not need to be referred to cabinet, but he declined to say if the prime minister approved of Theresa May's decision.

The prime minister's spokesman added that May would give a full statement to MPs on Monday afternoon, saying "the top civil servant had left his post and it is important to understand the reasons why". He insisted the prime minister had full confidence in May, a figure who is highly prized in Downing Street for managing so far to keep Home Office blunders to a minimum.

Labour has been demanding to know whether anyone posing a risk to national security entered Britain during the four months that the secret pilot scheme was allowed to run.

The shadow home secretary, Yvette Cooper, has written to May demanding that the independent inquiry that has been announced has a wide-enough remit to fully investigate "the actions of the Home Office, ministers and the effect of resource cuts on UKBA decision-making".

She is also pressing for the Home Office and UKBA to publish all documents and correspondence relating to the issue of passport checks.

Lucy Moreton, from the Immigration Services Union (ISU), one of the two UKBA unions, told BBC Radio 4's Today programme that staff "were not aware that the minister did not know" about checks being relaxed. "As far as staff were aware, this had been ministerially sanctioned," she said.

"It's a requirement. We aren't allowed to make that decision ourselves to relax those checks. It's for the discretion of the minister only."

Noting that May says she was unaware of the practice, Moreton added it was "entirely possible" that Clark or someone else at that level made the decision themselves.